dbNSFP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool dbNSFP
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Tool usage distribution map

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Associated diseases

This word cloud represents dbNSFP usage per disease context
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Protocols

dbNSFP specifications

Information


Unique identifier OMICS_00172
Name dbNSFP
Alternative name database for nonsynonymous SNPs' functional predictions
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Version 3.5
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline Xiaoming Liu

Publications for database for nonsynonymous SNPs' functional predictions

dbNSFP citations

 (147)
library_books

Incorporating epilepsy genetics into clinical practice: a 360°evaluation

2018
PMCID: 5945675
PMID: 29760947
DOI: 10.1038/s41525-018-0052-9

[…] mizygous state in the ExAC/gnomAD database were excluded in severe epileptic encephalopathy (EE) cases. All variants were submitted to prediction tools—predictions on protein level were obtained from dbNSFP Functional Predictions and Cores 3.0 database while the variants were submitted to bioinfomatic software tools, e.g., NNSplice and ESEfinder for predictions on transcriptional level. The ACMG g […]

library_books

VAReporter: variant reporter for cancer research of massive parallel sequencing

2018
BMC Genomics
PMCID: 5954270
PMID: 29764369
DOI: 10.1186/s12864-018-4468-5

[…] e most comprehensive list of support formats with respect to single and paired samples. A wide variety of biomedical databases, including dbSNP [], 1000 Genomes [], COSMIC, the Cancer Gene Census [], dbNSFP [], Clinvar [], OMIM [], RefSeq [], UniProt [], Pfam [], GO [], KEGG [], DrugBank [], the DGIdb [] and the Human Gene Mutation Database [] (HGMD), were compiled as local annotation databases to […]

library_books

Computational Protein Phenotype Characterization of IL10RA Mutations Causative to Early Onset Inflammatory Bowel Disease (IBD)

2018
Front Genet
PMCID: 5934427
PMID: 29755507
DOI: 10.3389/fgene.2018.00146

[…] To predict the deleterious nature of the mutants, we employed dbNSFP at Ensemble VEP (Variant Effect Predictor) (McLaren et al., ) which produces prediction scores for different algorithms like SIFT, PolyPhen 2.0, CADD, FATHMM, LRT, MetaLR, MetaSVM, PROVEAN, and […]

library_books

Rare variants in drug target genes contributing to complex diseases, phenome wide

2018
Sci Rep
PMCID: 5854600
PMID: 29545597
DOI: 10.1038/s41598-018-22834-4

[…] a transcript), a variant was considered to be LOF or non-synonymous if ANY annotation for that variant met our specification for LOF or non-synonymous. The following 5 scoring algorithms were used in dbNSFP to predict the deleterious variants (limited to only SNPs/SNVs):SIFT 5.2.2PolyPhen2 (HDIV training set)PolyPhen2 (HVAR training set)LRTMutationTaster.Functional annotation filter 3: LOF and pre […]

library_books

Whole exome sequencing in three families segregating a pediatric case of sarcoidosis

2018
BMC Med Genomics
PMCID: 5839022
PMID: 29510755
DOI: 10.1186/s12920-018-0338-x

[…] he deleterious effect of the prioritized variants, i.e., SIFT, PolyPhen, and CADD rank scores, against the other variants within the same gene []. The data showed no statistical differences for SIFT (dbNSFP_SIFT_rankscore: p = 0.4705) and POLYPHEN (dbNSFP_Polyphen2_HDIV_rankscore: p = 0.9322). We observed a statistically significant difference for the CADD score (dbNSFP_CADD_phred: p = 0.008468) ( […]

library_books

A combined linkage, microarray and exome analysis suggests MAP3K11 as a candidate gene for left ventricular hypertrophy

2018
BMC Med Genomics
PMCID: 5838853
PMID: 29506515
DOI: 10.1186/s12920-018-0339-9

[…] 1309 individuals. ECG and covariate data were available for 1072 of these samples. Further, for comparison and to predict the functionality of the variants, annotations were also performed using the dbNSFP (database of human non-synonymous SNPs and their functional predictions, http://varianttools.sourceforge.net/Annotation/DbNSFP) and Seattle (http://snp.gs.washington.edu/SeattleSeqAnnotation138 […]


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dbNSFP institution(s)
Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA; Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
dbNSFP funding source(s)
Supported by the US National Institutes of Health (5RC2HL102419 and U54HG003273).

dbNSFP reviews

 (2)
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ostrokach

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Dataset
Great dataset of SNP annotations.
Anonymous user #6211's avatar image No country

Anonymous user #6211

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Dataset
Works great with SnpEff for variant annotation.